A method of aligning a wafer includes recognizing images of the wafer accommodated on a work table and a notch of the wafer using a camera, designating at least one notch point of the notch in a recognized image, producing at least one reference line using the designated notch point in the recognized image, designating a center point of the reference line in the recognized image, producing an imaginary line having an angle with respect to the reference line from the center point of the reference line in the recognized image, producing a center line of the wafer using the imaginary line in the recognized image, and aligning the wafer using an alignment apparatus to allow the center line of the wafer and an alignment line of the work table to be matched.